SMET: Systematic Multiple Enzyme Targeting for Rational Design of Optimal Strains

Since the inception of metabolic engineering more than two decades ago, metabolic engineering has played a significant role in optimizing microbial biocatalysts and has had a significant impact on biotechnological applications related to health, food, energy, and environment. One of the key questions that metabolic engineers face is to identify which genes should be targeted to develop a robust and efficient strain to achieve desirable phenotypes, e.g., production of a target compound at high yields, titers, and productivities. We have developed a Systematic Multiple Enzyme Targeting method, called SMET¹, to rationally design optimal strains for target chemical overproduction. The SMET method combines both elementary mode analysis and ensemble metabolic modeling to derive SMET metrics including c-values and l-values that can identify rate-limiting reaction steps and suggest which enzymes and how much these enzymes to manipulate to enhance product yields, titers, and productivities. Here, we will present the application of the SMET method for analyzing Escherichia coli and Clostridium Thermocellum metabolic networks for aromatic acid and lignocellulosic ethanol overproduction.

¹Flowers, D., R. A. Thompson, D. Birdwell, T. Wang, and C. T. Trinh. 2013. SMET: systematic multiple enzyme targeting–a method to rationally design optimal strains for target chemical overproduction. Biotechnology Journal 8:605-618.